By default, Firefox 3 doesn't burn out bookmarks into an HTML file, preferring to keep them in its own local database. Because of this, Quicksilver will no longer pick up changes to your bookmarks once you upgrade to Firefox 3 (if you have set Quicksilver to index bookmarks).
To set Firefox to automatically export bookmarks to HTML, type "about:config" in the location bar and hit Enter. Type "export" into the filter field, and set "browser.bookmarks.autoExportHTML" to "true".